n-->pi* interactions in proteins.

Abstract

Hydrogen bonds between backbone amides are common in folded proteins. Here, we show that an intimate interaction between backbone amides also arises from the delocalization of a lone pair of electrons (n) from an oxygen atom to the antibonding orbital (pi*) of the subsequent carbonyl group. Natural bond orbital analysis predicted significant n-->pi* interactions in certain regions of the Ramachandran plot. These predictions were validated by a statistical analysis of a large, non-redundant subset of protein structures determined to high resolution. The correlation between these two independent studies is striking. Moreover, the n-->pi* interactions are abundant and especially prevalent in common secondary structures such as alpha-, 3(10)- and polyproline II helices and twisted beta-sheets. In addition to their evident effects on protein structure and stability, n-->pi* interactions could have important roles in protein folding and function, and merit inclusion in computational force fields.

a, Energy of the n→π* interactions for values of d and θ in the right-handed helical region of the Ramachandran plot (i.e., −180 ≤ φ ≤ 0; −180 ≤ ψ ≤ 0). The criteria in are obeyed within the gray rectangle. b, Frequency of values of d and θ among residue pairs (132149) in an α-helix (). c, Frequency of values of d and θ among residue pairs (221469) not in an α-helix (). Combined, the plots in panels b and c include all residue pairs (353618) in 1731 high-resolution structures; n.b., there are more data plotted here than are listed in , as the latter were culled for four-residue sequences, whereas as the data used in this figure were from residue pairs. The frequency of residue pairs with d ≤ 3.2 Å () emerge from the gray plane.

Potential n→π* interactions in the selectivity filter of the KcsA potassium ion channel

A single chain of the tetrameric channel determined at a high K+ concentration (PDB code 1k4c) structure was superposed on that determined at a low K+ concentration (PDB code 1k4d). Superpositions were carried out by the Secondary Structure Matching service at EBI (http://www.ebi.ac.uk/msd-srv/ssm).